my $s1 = "AYGTACTAGACTACAGACTACAGACATCTACAGACTCATCAGCAGCATATTTA";
my $s2 = "ACGTACTAGACTACAGACTACAGACATCTACAGACTCATCAGCAGCATATTKA";

my $s1_ = $s1;   $s1_ =~ tr/ACGT/\0/c;
my $s2_ = $s2;   $s2_ =~ tr/ACGT/\0/c;

my $merged = $s1 ^ $s1_ ^ $s2 ^ $s2_ | $s1_ & $s2_; 
say $merged;    # AYGTACTAGACTACAGACTACAGACATCTACAGACTCATCAGCAGCATATTKA